Scientists Create 3D Models of Cells in Minecraft for Educational and Research Purposes
Researchers have translated nanoscale experimental and computational data into precise 3D representations of bacteria, yeast, and human epithelial, breast, and breast cancer cells within the popular video game Minecraft. This innovation allows researchers and students of all ages to navigate biological cells, exploring their internal structures and observing the distribution of various components within the cell.
"CraftCells: A Window into Biological Cells" is the first broadly accessible tool providing users with an accurate 3D depiction of whole cells, according to Zaida (Zan) Luthey-Schulten, a professor of chemistry and physics at the University of Illinois Urbana-Champaign, who led the project. The team, which includes Illinois bioengineering professors Stephen Boppart and Rohit Bhargava, graduate student Kevin Tan, postdoctoral researchers Zane Thornburg and Seth Kenkel, and lead author Tianyu Wu, a biophysics graduate student, published their findings in the journal The Biophysicist.
Luthey-Schulten emphasized the importance of moving beyond 2D textbook images to experience the 3D organization of cells. While more intricate 3D visualizations of molecular data are accessible to some scientists through programs like NAMD and VMD, these require significant computing power, limiting their accessibility. CraftCells, however, offers a user-friendly and readily available 3D visualization platform.
The team utilized high-resolution microscopic data to construct their cell models, focusing on cells of particular interest to researchers and the public. Their initial 3D models include a yeast cell, epithelial cells from both cancerous and healthy breast tissue, and a "minimally viable" bacterial cell, stripped of non-essential genes.
These cellular worlds can be explored in 3D using a virtual reality headset. Players select from a menu of Minecraft worlds containing the desired cell type to begin their exploration. The bacterial cell stands out due to the absence of a nucleus, with DNA floating freely in the cytoplasm. The breast cancer cell exhibits visually distinct features, including an elongated and pointier shape and larger nucleoli within the nucleus compared to its healthy counterpart.
Tan explained that the elongated shape of a cancer cell is often associated with metastasis, indicating more aggressive cancers. Histopathologists also use the size of the nucleoli as a marker for cancer. CraftCells offers an educational and entertaining experience, with standard Minecraft tools and weapons modified to simulate real-world cellular events.
Players can experience the tissue-damaging effects of reactive oxygen species, ride a rollercoaster through DNA and cytoplasmic proteins in the bacterial cells, and even emulate laser ablation, a medical procedure, by shooting at breast cancer cells. The visualizations exclude certain molecules, such as water, to highlight prominent cellular structures. Features like proteins, DNA, and cell membranes can be toggled on and off to focus on specific components and understand their interactions.
The researchers carefully sized each 3D pixel, or voxel, to optimize the view of the cell. Voxel sizes range from one to 100 nanometers depending on the cell type. The researchers believe CraftCells can enhance scientific understanding by providing a more immersive and interactive 3D environment for studying cellular systems.
Thornburg highlighted the importance of 3D visualization in scientific research, emphasizing that CraftCells offers a unique level of 3D exploration not provided by other tools. Future iterations of CraftCells may allow scientists to explore different cell states, such as the uptake of targeted drugs by human cells or the changes occurring during ethanol production in yeast cells.
CraftCells is available free of charge and compatible with Minecraft Java, Bedrock, and Education editions. It can be downloaded from: https://github.com/Luthey-Schulten-Lab/CraftCells.
Luthey-Schulten, Boppart, and Bhargava are professors at the Beckman Institute for Advanced Science and Technology. Bhargava is the director of the Cancer Center in Illinois. This work was conducted at the National Science Foundation Science and Technology Center for Quantitative Cell Biology in the Beckman Institute at the University of Illinois Urbana-Champaign.